vcf_clone_detect.py results for P. acuta RNA-seq samplesSetup R env. Load packages and set default image export formats, size and resolution.
knitr::opts_chunk$set(echo = TRUE,
fig.height = 12,
fig.width = 12,
dev = c("png", "pdf"),
dpi = 1000)
library(readxl)
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
library(ggplot2)
library(gplots)
##
## Attaching package: 'gplots'
## The following object is masked from 'package:stats':
##
## lowess
library(reshape2)
library(RcppCNPy)
library(tibble)
library(ggdendro)
library(cowplot)
library(RColorBrewer)
library(viridis)
## Loading required package: viridisLite
library(knitr)
library(plotly)
##
## Attaching package: 'plotly'
## The following object is masked from 'package:ggplot2':
##
## last_plot
## The following object is masked from 'package:stats':
##
## filter
## The following object is masked from 'package:graphics':
##
## layout
library(phylogram)
options(scipen = 999) #Prevent scientific notation
cexSize <- 0.3
Load file with annotation for each sample.
samples.info <- read.table("../../samples_Pacuta.annotations.txt", header=T, comment.char='')
rownames(samples.info) <- samples.info$sample
samples.info
## sample species treatment timepoint plugid
## Pacuta_ATAC_TP11_1777 Pacuta_ATAC_TP11_1777 Pacuta ATAC TP11 1777
## Pacuta_ATAC_TP8_1051 Pacuta_ATAC_TP8_1051 Pacuta ATAC TP8 1051
## Pacuta_ATHC_TP4_2733 Pacuta_ATHC_TP4_2733 Pacuta ATHC TP4 2733
## Pacuta_ATHC_TP8_1459 Pacuta_ATHC_TP8_1459 Pacuta ATHC TP8 1459
## Pacuta_HTAC_TP3_1642 Pacuta_HTAC_TP3_1642 Pacuta HTAC TP3 1642
## Pacuta_HTAC_TP4_1767 Pacuta_HTAC_TP4_1767 Pacuta HTAC TP4 1767
## Pacuta_HTAC_TP7_2072 Pacuta_HTAC_TP7_2072 Pacuta HTAC TP7 2072
## Pacuta_ATAC_TP11_1103 Pacuta_ATAC_TP11_1103 Pacuta ATAC TP11 1103
## Pacuta_ATAC_TP11_2306 Pacuta_ATAC_TP11_2306 Pacuta ATAC TP11 2306
## Pacuta_ATAC_TP3_1041 Pacuta_ATAC_TP3_1041 Pacuta ATAC TP3 1041
## Pacuta_ATAC_TP3_1637 Pacuta_ATAC_TP3_1637 Pacuta ATAC TP3 1637
## Pacuta_ATAC_TP4_1762 Pacuta_ATAC_TP4_1762 Pacuta ATAC TP4 1762
## Pacuta_ATAC_TP7_2413 Pacuta_ATAC_TP7_2413 Pacuta ATAC TP7 2413
## Pacuta_ATAC_TP8_2012 Pacuta_ATAC_TP8_2012 Pacuta ATAC TP8 2012
## Pacuta_ATAC_TP9_2357 Pacuta_ATAC_TP9_2357 Pacuta ATAC TP9 2357
## Pacuta_ATHC_TP11_1147 Pacuta_ATHC_TP11_1147 Pacuta ATHC TP11 1147
## Pacuta_ATHC_TP3_2534 Pacuta_ATHC_TP3_2534 Pacuta ATHC TP3 2534
## Pacuta_ATHC_TP4_1220 Pacuta_ATHC_TP4_1220 Pacuta ATHC TP4 1220
## Pacuta_ATHC_TP5_2877 Pacuta_ATHC_TP5_2877 Pacuta ATHC TP5 2877
## Pacuta_ATHC_TP6_2870 Pacuta_ATHC_TP6_2870 Pacuta ATHC TP6 2870
## Pacuta_ATHC_TP7_2878 Pacuta_ATHC_TP7_2878 Pacuta ATHC TP7 2878
## Pacuta_ATHC_TP9_1451 Pacuta_ATHC_TP9_1451 Pacuta ATHC TP9 1451
## Pacuta_ATHC_TP9_2873 Pacuta_ATHC_TP9_2873 Pacuta ATHC TP9 2873
## Pacuta_HTAC_TP10_2064 Pacuta_HTAC_TP10_2064 Pacuta HTAC TP10 2064
## Pacuta_HTAC_TP11_1596 Pacuta_HTAC_TP11_1596 Pacuta HTAC TP11 1596
## Pacuta_HTAC_TP1_2414 Pacuta_HTAC_TP1_2414 Pacuta HTAC TP1 2414
## Pacuta_HTAC_TP5_1707 Pacuta_HTAC_TP5_1707 Pacuta HTAC TP5 1707
## Pacuta_HTAC_TP6_1466 Pacuta_HTAC_TP6_1466 Pacuta HTAC TP6 1466
## Pacuta_HTAC_TP7_1728 Pacuta_HTAC_TP7_1728 Pacuta HTAC TP7 1728
## Pacuta_HTAC_TP8_2513 Pacuta_HTAC_TP8_2513 Pacuta HTAC TP8 2513
## Pacuta_HTAC_TP9_1696 Pacuta_HTAC_TP9_1696 Pacuta HTAC TP9 1696
## Pacuta_HTHC_TP10_2300 Pacuta_HTHC_TP10_2300 Pacuta HTHC TP10 2300
## Pacuta_HTHC_TP3_1227 Pacuta_HTHC_TP3_1227 Pacuta HTHC TP3 1227
## Pacuta_HTHC_TP5_2087 Pacuta_HTHC_TP5_2087 Pacuta HTHC TP5 2087
## Pacuta_HTHC_TP6_1138 Pacuta_HTHC_TP6_1138 Pacuta HTHC TP6 1138
## Pacuta_HTHC_TP6_1595 Pacuta_HTHC_TP6_1595 Pacuta HTHC TP6 1595
## Pacuta_HTHC_TP8_1709 Pacuta_HTHC_TP8_1709 Pacuta HTHC TP8 1709
## Pacuta_HTHC_TP8_2304 Pacuta_HTHC_TP8_2304 Pacuta HTHC TP8 2304
## Pacuta_HTHC_TP9_1131 Pacuta_HTHC_TP9_1131 Pacuta HTHC TP9 1131
## Pacuta_HTHC_TP9_2202 Pacuta_HTHC_TP9_2202 Pacuta HTHC TP9 2202
## Pacuta_HTHC_TP9_2305 Pacuta_HTHC_TP9_2305 Pacuta HTHC TP9 2305
## Pacuta_ATAC_TP10_1559 Pacuta_ATAC_TP10_1559 Pacuta ATAC TP10 1559
## Pacuta_ATAC_TP10_1641 Pacuta_ATAC_TP10_1641 Pacuta ATAC TP10 1641
## Pacuta_ATAC_TP1_2363 Pacuta_ATAC_TP1_2363 Pacuta ATAC TP1 2363
## Pacuta_ATAC_TP3_1471 Pacuta_ATAC_TP3_1471 Pacuta ATAC TP3 1471
## Pacuta_ATAC_TP4_1060 Pacuta_ATAC_TP4_1060 Pacuta ATAC TP4 1060
## Pacuta_ATAC_TP4_2002 Pacuta_ATAC_TP4_2002 Pacuta ATAC TP4 2002
## Pacuta_ATAC_TP5_1563 Pacuta_ATAC_TP5_1563 Pacuta ATAC TP5 1563
## Pacuta_ATAC_TP5_1757 Pacuta_ATAC_TP5_1757 Pacuta ATAC TP5 1757
## Pacuta_ATAC_TP9_1594 Pacuta_ATAC_TP9_1594 Pacuta ATAC TP9 1594
## Pacuta_ATHC_TP7_2409 Pacuta_ATHC_TP7_2409 Pacuta ATHC TP7 2409
## Pacuta_ATHC_TP8_2564 Pacuta_ATHC_TP8_2564 Pacuta ATHC TP8 2564
## Pacuta_HTAC_TP10_1536 Pacuta_HTAC_TP10_1536 Pacuta HTAC TP10 1536
## Pacuta_HTAC_TP11_1582 Pacuta_HTAC_TP11_1582 Pacuta HTAC TP11 1582
## Pacuta_HTAC_TP11_1647 Pacuta_HTAC_TP11_1647 Pacuta HTAC TP11 1647
## Pacuta_HTAC_TP1_2005 Pacuta_HTAC_TP1_2005 Pacuta HTAC TP1 2005
## Pacuta_HTAC_TP3_1617 Pacuta_HTAC_TP3_1617 Pacuta HTAC TP3 1617
## Pacuta_HTAC_TP4_1701 Pacuta_HTAC_TP4_1701 Pacuta HTAC TP4 1701
## Pacuta_HTAC_TP8_1765 Pacuta_HTAC_TP8_1765 Pacuta HTAC TP8 1765
## Pacuta_HTHC_TP10_1238 Pacuta_HTHC_TP10_1238 Pacuta HTHC TP10 1238
## Pacuta_HTHC_TP10_1732 Pacuta_HTHC_TP10_1732 Pacuta HTHC TP10 1732
## Pacuta_HTHC_TP1_1239 Pacuta_HTHC_TP1_1239 Pacuta HTHC TP1 1239
## Pacuta_HTHC_TP4_2195 Pacuta_HTHC_TP4_2195 Pacuta HTHC TP4 2195
## Pacuta_HTHC_TP7_1090 Pacuta_HTHC_TP7_1090 Pacuta HTHC TP7 1090
## Pacuta_HTHC_TP7_1820 Pacuta_HTHC_TP7_1820 Pacuta HTHC TP7 1820
## Pacuta_ATAC_TP1_1043 Pacuta_ATAC_TP1_1043 Pacuta ATAC TP1 1043
## Pacuta_ATAC_TP6_1542 Pacuta_ATAC_TP6_1542 Pacuta ATAC TP6 1542
## Pacuta_ATHC_TP1_2743 Pacuta_ATHC_TP1_2743 Pacuta ATHC TP1 2743
## Pacuta_ATHC_TP3_2750 Pacuta_ATHC_TP3_2750 Pacuta ATHC TP3 2750
## Pacuta_HTAC_TP4_1581 Pacuta_HTAC_TP4_1581 Pacuta HTAC TP4 1581
## Pacuta_HTHC_TP4_1343 Pacuta_HTHC_TP4_1343 Pacuta HTHC TP4 1343
## Pacuta_HTHC_TP7_1427 Pacuta_HTHC_TP7_1427 Pacuta HTHC TP7 1427
## Pacuta_HTHC_TP8_1184 Pacuta_HTHC_TP8_1184 Pacuta HTHC TP8 1184
## Pacuta_ATAC_TP10_1159 Pacuta_ATAC_TP10_1159 Pacuta ATAC TP10 1159
## Pacuta_ATAC_TP1_1775 Pacuta_ATAC_TP1_1775 Pacuta ATAC TP1 1775
## Pacuta_ATAC_TP6_1468 Pacuta_ATAC_TP6_1468 Pacuta ATAC TP6 1468
## Pacuta_ATAC_TP8_1755 Pacuta_ATAC_TP8_1755 Pacuta ATAC TP8 1755
## Pacuta_ATAC_TP9_1141 Pacuta_ATAC_TP9_1141 Pacuta ATAC TP9 1141
## Pacuta_ATHC_TP5_2212 Pacuta_ATHC_TP5_2212 Pacuta ATHC TP5 2212
## Pacuta_HTAC_TP6_1744 Pacuta_HTAC_TP6_1744 Pacuta HTAC TP6 1744
## Pacuta_HTAC_TP9_1302 Pacuta_HTAC_TP9_1302 Pacuta HTAC TP9 1302
## Pacuta_HTAC_TP9_1486 Pacuta_HTAC_TP9_1486 Pacuta HTAC TP9 1486
## Pacuta_ATAC_TP6_1050 Pacuta_ATAC_TP6_1050 Pacuta ATAC TP6 1050
## Pacuta_ATAC_TP7_1047 Pacuta_ATAC_TP7_1047 Pacuta ATAC TP7 1047
## Pacuta_ATHC_TP10_2197 Pacuta_ATHC_TP10_2197 Pacuta ATHC TP10 2197
## Pacuta_ATHC_TP1_1207 Pacuta_ATHC_TP1_1207 Pacuta ATHC TP1 1207
## Pacuta_ATHC_TP11_2668 Pacuta_ATHC_TP11_2668 Pacuta ATHC TP11 2668
## Pacuta_ATHC_TP11_2879 Pacuta_ATHC_TP11_2879 Pacuta ATHC TP11 2879
## Pacuta_ATHC_TP1_2977 Pacuta_ATHC_TP1_2977 Pacuta ATHC TP1 2977
## Pacuta_ATHC_TP3_1219 Pacuta_ATHC_TP3_1219 Pacuta ATHC TP3 1219
## Pacuta_ATHC_TP4_2993 Pacuta_ATHC_TP4_2993 Pacuta ATHC TP4 2993
## Pacuta_ATHC_TP5_1296 Pacuta_ATHC_TP5_1296 Pacuta ATHC TP5 1296
## Pacuta_ATHC_TP6_2999 Pacuta_ATHC_TP6_2999 Pacuta ATHC TP6 2999
## Pacuta_ATHC_TP7_1281 Pacuta_ATHC_TP7_1281 Pacuta ATHC TP7 1281
## Pacuta_ATHC_TP8_2861 Pacuta_ATHC_TP8_2861 Pacuta ATHC TP8 2861
## Pacuta_ATHC_TP9_2979 Pacuta_ATHC_TP9_2979 Pacuta ATHC TP9 2979
## Pacuta_HTAC_TP10_1225 Pacuta_HTAC_TP10_1225 Pacuta HTAC TP10 1225
## Pacuta_HTAC_TP3_2026 Pacuta_HTAC_TP3_2026 Pacuta HTAC TP3 2026
## Pacuta_HTAC_TP5_1303 Pacuta_HTAC_TP5_1303 Pacuta HTAC TP5 1303
## Pacuta_HTAC_TP5_1571 Pacuta_HTAC_TP5_1571 Pacuta HTAC TP5 1571
## Pacuta_HTAC_TP6_1330 Pacuta_HTAC_TP6_1330 Pacuta HTAC TP6 1330
## Pacuta_HTAC_TP7_1487 Pacuta_HTAC_TP7_1487 Pacuta HTAC TP7 1487
## Pacuta_HTAC_TP8_1329 Pacuta_HTAC_TP8_1329 Pacuta HTAC TP8 1329
## Pacuta_HTHC_TP11_1416 Pacuta_HTHC_TP11_1416 Pacuta HTHC TP11 1416
## Pacuta_HTHC_TP1_1676 Pacuta_HTHC_TP1_1676 Pacuta HTHC TP1 1676
## Pacuta_HTHC_TP3_1418 Pacuta_HTHC_TP3_1418 Pacuta HTHC TP3 1418
## Pacuta_HTHC_TP3_2527 Pacuta_HTHC_TP3_2527 Pacuta HTHC TP3 2527
## Pacuta_HTHC_TP4_1169 Pacuta_HTHC_TP4_1169 Pacuta HTHC TP4 1169
## Pacuta_HTHC_TP5_1168 Pacuta_HTHC_TP5_1168 Pacuta HTHC TP5 1168
## Pacuta_ATAC_TP5_1059 Pacuta_ATAC_TP5_1059 Pacuta ATAC TP5 1059
## Pacuta_HTHC_TP1_2210 Pacuta_HTHC_TP1_2210 Pacuta HTHC TP1 2210
## Pacuta_HTAC_TP1_1653 Pacuta_HTAC_TP1_1653 Pacuta HTAC TP1 1653
## Pacuta_HTHC_TP6_1721 Pacuta_HTHC_TP6_1721 Pacuta HTHC TP6 1721
## Pacuta_ATAC_TP7_1445 Pacuta_ATAC_TP7_1445 Pacuta ATAC TP7 1445
## Pacuta_ATHC_TP10_1205 Pacuta_ATHC_TP10_1205 Pacuta ATHC TP10 1205
## Pacuta_ATHC_TP10_2550 Pacuta_ATHC_TP10_2550 Pacuta ATHC TP10 2550
## Pacuta_ATHC_TP6_1254 Pacuta_ATHC_TP6_1254 Pacuta ATHC TP6 1254
## Pacuta_HTHC_TP11_2185 Pacuta_HTHC_TP11_2185 Pacuta HTHC TP11 2185
## Pacuta_HTHC_TP5_1415 Pacuta_HTHC_TP5_1415 Pacuta HTHC TP5 1415
## reef reef_color ploidy ploidy_color group
## Pacuta_ATAC_TP11_1777 HIMB #b35806 3 #d95f02 Group1
## Pacuta_ATAC_TP8_1051 Reef.11.13 #fee0b6 3 #d95f02 Group1
## Pacuta_ATHC_TP4_2733 Reef.42.43 #542788 3 #d95f02 Group1
## Pacuta_ATHC_TP8_1459 Reef.18 #d8daeb 3 #d95f02 Group1
## Pacuta_HTAC_TP3_1642 HIMB #b35806 3 #d95f02 Group1
## Pacuta_HTAC_TP4_1767 Reef.42.43 #542788 3 #d95f02 Group1
## Pacuta_HTAC_TP7_2072 HIMB #b35806 3 #d95f02 Group1
## Pacuta_ATAC_TP11_1103 Reef.42.43 #542788 3 #d95f02 Group2
## Pacuta_ATAC_TP11_2306 Reef.18 #d8daeb 3 #d95f02 Group2
## Pacuta_ATAC_TP3_1041 Reef.11.13 #fee0b6 3 #d95f02 Group2
## Pacuta_ATAC_TP3_1637 Reef.11.13 #fee0b6 3 #d95f02 Group2
## Pacuta_ATAC_TP4_1762 Reef.42.43 #542788 3 #d95f02 Group2
## Pacuta_ATAC_TP7_2413 Reef.18 #d8daeb 3 #d95f02 Group2
## Pacuta_ATAC_TP8_2012 Reef.42.43 #542788 3 #d95f02 Group2
## Pacuta_ATAC_TP9_2357 Reef.18 #d8daeb 3 #d95f02 Group2
## Pacuta_ATHC_TP11_1147 HIMB #b35806 3 #d95f02 Group2
## Pacuta_ATHC_TP3_2534 Reef.18 #d8daeb 3 #d95f02 Group2
## Pacuta_ATHC_TP4_1220 Lilipuna.Fringe #f1a340 3 #d95f02 Group2
## Pacuta_ATHC_TP5_2877 HIMB #b35806 3 #d95f02 Group2
## Pacuta_ATHC_TP6_2870 HIMB #b35806 3 #d95f02 Group2
## Pacuta_ATHC_TP7_2878 HIMB #b35806 3 #d95f02 Group2
## Pacuta_ATHC_TP9_1451 Reef.18 #d8daeb 3 #d95f02 Group2
## Pacuta_ATHC_TP9_2873 HIMB #b35806 3 #d95f02 Group2
## Pacuta_HTAC_TP10_2064 HIMB #b35806 3 #d95f02 Group2
## Pacuta_HTAC_TP11_1596 Reef.42.43 #542788 3 #d95f02 Group2
## Pacuta_HTAC_TP1_2414 Reef.18 #d8daeb 3 #d95f02 Group2
## Pacuta_HTAC_TP5_1707 Reef.11.13 #fee0b6 3 #d95f02 Group2
## Pacuta_HTAC_TP6_1466 Lilipuna.Fringe #f1a340 3 #d95f02 Group2
## Pacuta_HTAC_TP7_1728 Reef.18 #d8daeb 3 #d95f02 Group2
## Pacuta_HTAC_TP8_2513 Reef.18 #d8daeb 3 #d95f02 Group2
## Pacuta_HTAC_TP9_1696 Lilipuna.Fringe #f1a340 3 #d95f02 Group2
## Pacuta_HTHC_TP10_2300 Reef.18 #d8daeb 3 #d95f02 Group2
## Pacuta_HTHC_TP3_1227 Reef.42.43 #542788 3 #d95f02 Group2
## Pacuta_HTHC_TP5_2087 HIMB #b35806 3 #d95f02 Group2
## Pacuta_HTHC_TP6_1138 HIMB #b35806 3 #d95f02 Group2
## Pacuta_HTHC_TP6_1595 HIMB #b35806 3 #d95f02 Group2
## Pacuta_HTHC_TP8_1709 Lilipuna.Fringe #f1a340 3 #d95f02 Group2
## Pacuta_HTHC_TP8_2304 Reef.18 #d8daeb 3 #d95f02 Group2
## Pacuta_HTHC_TP9_1131 HIMB #b35806 3 #d95f02 Group2
## Pacuta_HTHC_TP9_2202 HIMB #b35806 3 #d95f02 Group2
## Pacuta_HTHC_TP9_2305 Reef.18 #d8daeb 3 #d95f02 Group2
## Pacuta_ATAC_TP10_1559 Lilipuna.Fringe #f1a340 3 #d95f02 Group3
## Pacuta_ATAC_TP10_1641 HIMB #b35806 3 #d95f02 Group3
## Pacuta_ATAC_TP1_2363 Reef.18 #d8daeb 3 #d95f02 Group3
## Pacuta_ATAC_TP3_1471 Reef.35.36 #998ec3 3 #d95f02 Group3
## Pacuta_ATAC_TP4_1060 Reef.18 #d8daeb 3 #d95f02 Group3
## Pacuta_ATAC_TP4_2002 Reef.42.43 #542788 3 #d95f02 Group3
## Pacuta_ATAC_TP5_1563 Lilipuna.Fringe #f1a340 3 #d95f02 Group3
## Pacuta_ATAC_TP5_1757 Reef.42.43 #542788 3 #d95f02 Group3
## Pacuta_ATAC_TP9_1594 Reef.35.36 #998ec3 3 #d95f02 Group3
## Pacuta_ATHC_TP7_2409 Lilipuna.Fringe #f1a340 3 #d95f02 Group3
## Pacuta_ATHC_TP8_2564 Reef.18 #d8daeb 3 #d95f02 Group3
## Pacuta_HTAC_TP10_1536 Reef.35.36 #998ec3 3 #d95f02 Group3
## Pacuta_HTAC_TP11_1582 Lilipuna.Fringe #f1a340 3 #d95f02 Group3
## Pacuta_HTAC_TP11_1647 HIMB #b35806 3 #d95f02 Group3
## Pacuta_HTAC_TP1_2005 Reef.18 #d8daeb 3 #d95f02 Group3
## Pacuta_HTAC_TP3_1617 Reef.42.43 #542788 3 #d95f02 Group3
## Pacuta_HTAC_TP4_1701 Reef.18 #d8daeb 3 #d95f02 Group3
## Pacuta_HTAC_TP8_1765 Reef.42.43 #542788 3 #d95f02 Group3
## Pacuta_HTHC_TP10_1238 Reef.42.43 #542788 3 #d95f02 Group3
## Pacuta_HTHC_TP10_1732 Lilipuna.Fringe #f1a340 3 #d95f02 Group3
## Pacuta_HTHC_TP1_1239 Reef.42.43 #542788 3 #d95f02 Group3
## Pacuta_HTHC_TP4_2195 Reef.42.43 #542788 3 #d95f02 Group3
## Pacuta_HTHC_TP7_1090 Lilipuna.Fringe #f1a340 3 #d95f02 Group3
## Pacuta_HTHC_TP7_1820 Reef.11.13 #fee0b6 3 #d95f02 Group3
## Pacuta_ATAC_TP1_1043 Lilipuna.Fringe #f1a340 3 #d95f02 Group4
## Pacuta_ATAC_TP6_1542 Lilipuna.Fringe #f1a340 3 #d95f02 Group4
## Pacuta_ATHC_TP1_2743 Lilipuna.Fringe #f1a340 3 #d95f02 Group4
## Pacuta_ATHC_TP3_2750 Reef.42.43 #542788 3 #d95f02 Group4
## Pacuta_HTAC_TP4_1581 Lilipuna.Fringe #f1a340 3 #d95f02 Group4
## Pacuta_HTHC_TP4_1343 Lilipuna.Fringe #f1a340 3 #d95f02 Group4
## Pacuta_HTHC_TP7_1427 Lilipuna.Fringe #f1a340 3 #d95f02 Group4
## Pacuta_HTHC_TP8_1184 Lilipuna.Fringe #f1a340 3 #d95f02 Group4
## Pacuta_ATAC_TP10_1159 Reef.42.43 #542788 2 #1b9e77 Group5
## Pacuta_ATAC_TP1_1775 Reef.42.43 #542788 2 #1b9e77 Group5
## Pacuta_ATAC_TP6_1468 Reef.35.36 #998ec3 2 #1b9e77 Group5
## Pacuta_ATAC_TP8_1755 Reef.42.43 #542788 2 #1b9e77 Group5
## Pacuta_ATAC_TP9_1141 Reef.42.43 #542788 2 #1b9e77 Group5
## Pacuta_ATHC_TP5_2212 Reef.35.36 #998ec3 2 #1b9e77 Group5
## Pacuta_HTAC_TP6_1744 Reef.35.36 #998ec3 2 #1b9e77 Group5
## Pacuta_HTAC_TP9_1302 Reef.35.36 #998ec3 2 #1b9e77 Group5
## Pacuta_HTAC_TP9_1486 Reef.11.13 #fee0b6 2 #1b9e77 Group5
## Pacuta_ATAC_TP6_1050 Reef.18 #d8daeb 2 #1b9e77 Group6
## Pacuta_ATAC_TP7_1047 Lilipuna.Fringe #f1a340 2 #1b9e77 Group6
## Pacuta_ATHC_TP10_2197 Reef.35.36 #998ec3 2 #1b9e77 Group6
## Pacuta_ATHC_TP1_1207 Reef.11.13 #fee0b6 2 #1b9e77 Group6
## Pacuta_ATHC_TP11_2668 Lilipuna.Fringe #f1a340 2 #1b9e77 Group6
## Pacuta_ATHC_TP11_2879 HIMB #b35806 2 #1b9e77 Group6
## Pacuta_ATHC_TP1_2977 Reef.11.13 #fee0b6 2 #1b9e77 Group6
## Pacuta_ATHC_TP3_1219 Reef.35.36 #998ec3 2 #1b9e77 Group6
## Pacuta_ATHC_TP4_2993 Reef.11.13 #fee0b6 2 #1b9e77 Group6
## Pacuta_ATHC_TP5_1296 Reef.11.13 #fee0b6 2 #1b9e77 Group6
## Pacuta_ATHC_TP6_2999 Lilipuna.Fringe #f1a340 2 #1b9e77 Group6
## Pacuta_ATHC_TP7_1281 Reef.35.36 #998ec3 2 #1b9e77 Group6
## Pacuta_ATHC_TP8_2861 HIMB #b35806 2 #1b9e77 Group6
## Pacuta_ATHC_TP9_2979 Reef.35.36 #998ec3 2 #1b9e77 Group6
## Pacuta_HTAC_TP10_1225 HIMB #b35806 2 #1b9e77 Group6
## Pacuta_HTAC_TP3_2026 Reef.42.43 #542788 2 #1b9e77 Group6
## Pacuta_HTAC_TP5_1303 Reef.35.36 #998ec3 2 #1b9e77 Group6
## Pacuta_HTAC_TP5_1571 Reef.35.36 #998ec3 2 #1b9e77 Group6
## Pacuta_HTAC_TP6_1330 Reef.35.36 #998ec3 2 #1b9e77 Group6
## Pacuta_HTAC_TP7_1487 Lilipuna.Fringe #f1a340 2 #1b9e77 Group6
## Pacuta_HTAC_TP8_1329 Lilipuna.Fringe #f1a340 2 #1b9e77 Group6
## Pacuta_HTHC_TP11_1416 Reef.11.13 #fee0b6 2 #1b9e77 Group6
## Pacuta_HTHC_TP1_1676 Reef.42.43 #542788 2 #1b9e77 Group6
## Pacuta_HTHC_TP3_1418 Lilipuna.Fringe #f1a340 2 #1b9e77 Group6
## Pacuta_HTHC_TP3_2527 Reef.18 #d8daeb 2 #1b9e77 Group6
## Pacuta_HTHC_TP4_1169 Reef.35.36 #998ec3 2 #1b9e77 Group6
## Pacuta_HTHC_TP5_1168 Reef.35.36 #998ec3 2 #1b9e77 Group6
## Pacuta_ATAC_TP5_1059 Reef.11.13 #fee0b6 2 #1b9e77 Group7
## Pacuta_HTHC_TP1_2210 Reef.42.43 #542788 2 #1b9e77 Group7
## Pacuta_HTAC_TP1_1653 HIMB #b35806 2 #1b9e77 Group8
## Pacuta_HTHC_TP6_1721 Lilipuna.Fringe #f1a340 2 #1b9e77 Group8
## Pacuta_ATAC_TP7_1445 Reef.11.13 #fee0b6 2 #1b9e77 Ungroup
## Pacuta_ATHC_TP10_1205 Reef.35.36 #998ec3 2 #1b9e77 Ungroup
## Pacuta_ATHC_TP10_2550 Reef.18 #d8daeb 2 #1b9e77 Ungroup
## Pacuta_ATHC_TP6_1254 Reef.42.43 #542788 3 #d95f02 Ungroup
## Pacuta_HTHC_TP11_2185 HIMB #b35806 3 #d95f02 Ungroup
## Pacuta_HTHC_TP5_1415 Reef.11.13 #fee0b6 2 #1b9e77 Ungroup
## group_color
## Pacuta_ATAC_TP11_1777 #1f78b4
## Pacuta_ATAC_TP8_1051 #1f78b4
## Pacuta_ATHC_TP4_2733 #1f78b4
## Pacuta_ATHC_TP8_1459 #1f78b4
## Pacuta_HTAC_TP3_1642 #1f78b4
## Pacuta_HTAC_TP4_1767 #1f78b4
## Pacuta_HTAC_TP7_2072 #1f78b4
## Pacuta_ATAC_TP11_1103 #33a02c
## Pacuta_ATAC_TP11_2306 #33a02c
## Pacuta_ATAC_TP3_1041 #33a02c
## Pacuta_ATAC_TP3_1637 #33a02c
## Pacuta_ATAC_TP4_1762 #33a02c
## Pacuta_ATAC_TP7_2413 #33a02c
## Pacuta_ATAC_TP8_2012 #33a02c
## Pacuta_ATAC_TP9_2357 #33a02c
## Pacuta_ATHC_TP11_1147 #33a02c
## Pacuta_ATHC_TP3_2534 #33a02c
## Pacuta_ATHC_TP4_1220 #33a02c
## Pacuta_ATHC_TP5_2877 #33a02c
## Pacuta_ATHC_TP6_2870 #33a02c
## Pacuta_ATHC_TP7_2878 #33a02c
## Pacuta_ATHC_TP9_1451 #33a02c
## Pacuta_ATHC_TP9_2873 #33a02c
## Pacuta_HTAC_TP10_2064 #33a02c
## Pacuta_HTAC_TP11_1596 #33a02c
## Pacuta_HTAC_TP1_2414 #33a02c
## Pacuta_HTAC_TP5_1707 #33a02c
## Pacuta_HTAC_TP6_1466 #33a02c
## Pacuta_HTAC_TP7_1728 #33a02c
## Pacuta_HTAC_TP8_2513 #33a02c
## Pacuta_HTAC_TP9_1696 #33a02c
## Pacuta_HTHC_TP10_2300 #33a02c
## Pacuta_HTHC_TP3_1227 #33a02c
## Pacuta_HTHC_TP5_2087 #33a02c
## Pacuta_HTHC_TP6_1138 #33a02c
## Pacuta_HTHC_TP6_1595 #33a02c
## Pacuta_HTHC_TP8_1709 #33a02c
## Pacuta_HTHC_TP8_2304 #33a02c
## Pacuta_HTHC_TP9_1131 #33a02c
## Pacuta_HTHC_TP9_2202 #33a02c
## Pacuta_HTHC_TP9_2305 #33a02c
## Pacuta_ATAC_TP10_1559 #c51b7d
## Pacuta_ATAC_TP10_1641 #c51b7d
## Pacuta_ATAC_TP1_2363 #c51b7d
## Pacuta_ATAC_TP3_1471 #c51b7d
## Pacuta_ATAC_TP4_1060 #c51b7d
## Pacuta_ATAC_TP4_2002 #c51b7d
## Pacuta_ATAC_TP5_1563 #c51b7d
## Pacuta_ATAC_TP5_1757 #c51b7d
## Pacuta_ATAC_TP9_1594 #c51b7d
## Pacuta_ATHC_TP7_2409 #c51b7d
## Pacuta_ATHC_TP8_2564 #c51b7d
## Pacuta_HTAC_TP10_1536 #c51b7d
## Pacuta_HTAC_TP11_1582 #c51b7d
## Pacuta_HTAC_TP11_1647 #c51b7d
## Pacuta_HTAC_TP1_2005 #c51b7d
## Pacuta_HTAC_TP3_1617 #c51b7d
## Pacuta_HTAC_TP4_1701 #c51b7d
## Pacuta_HTAC_TP8_1765 #c51b7d
## Pacuta_HTHC_TP10_1238 #c51b7d
## Pacuta_HTHC_TP10_1732 #c51b7d
## Pacuta_HTHC_TP1_1239 #c51b7d
## Pacuta_HTHC_TP4_2195 #c51b7d
## Pacuta_HTHC_TP7_1090 #c51b7d
## Pacuta_HTHC_TP7_1820 #c51b7d
## Pacuta_ATAC_TP1_1043 #6a3d9a
## Pacuta_ATAC_TP6_1542 #6a3d9a
## Pacuta_ATHC_TP1_2743 #6a3d9a
## Pacuta_ATHC_TP3_2750 #6a3d9a
## Pacuta_HTAC_TP4_1581 #6a3d9a
## Pacuta_HTHC_TP4_1343 #6a3d9a
## Pacuta_HTHC_TP7_1427 #6a3d9a
## Pacuta_HTHC_TP8_1184 #6a3d9a
## Pacuta_ATAC_TP10_1159 #ff7f00
## Pacuta_ATAC_TP1_1775 #ff7f00
## Pacuta_ATAC_TP6_1468 #ff7f00
## Pacuta_ATAC_TP8_1755 #ff7f00
## Pacuta_ATAC_TP9_1141 #ff7f00
## Pacuta_ATHC_TP5_2212 #ff7f00
## Pacuta_HTAC_TP6_1744 #ff7f00
## Pacuta_HTAC_TP9_1302 #ff7f00
## Pacuta_HTAC_TP9_1486 #ff7f00
## Pacuta_ATAC_TP6_1050 #e31a1c
## Pacuta_ATAC_TP7_1047 #e31a1c
## Pacuta_ATHC_TP10_2197 #e31a1c
## Pacuta_ATHC_TP1_1207 #e31a1c
## Pacuta_ATHC_TP11_2668 #e31a1c
## Pacuta_ATHC_TP11_2879 #e31a1c
## Pacuta_ATHC_TP1_2977 #e31a1c
## Pacuta_ATHC_TP3_1219 #e31a1c
## Pacuta_ATHC_TP4_2993 #e31a1c
## Pacuta_ATHC_TP5_1296 #e31a1c
## Pacuta_ATHC_TP6_2999 #e31a1c
## Pacuta_ATHC_TP7_1281 #e31a1c
## Pacuta_ATHC_TP8_2861 #e31a1c
## Pacuta_ATHC_TP9_2979 #e31a1c
## Pacuta_HTAC_TP10_1225 #e31a1c
## Pacuta_HTAC_TP3_2026 #e31a1c
## Pacuta_HTAC_TP5_1303 #e31a1c
## Pacuta_HTAC_TP5_1571 #e31a1c
## Pacuta_HTAC_TP6_1330 #e31a1c
## Pacuta_HTAC_TP7_1487 #e31a1c
## Pacuta_HTAC_TP8_1329 #e31a1c
## Pacuta_HTHC_TP11_1416 #e31a1c
## Pacuta_HTHC_TP1_1676 #e31a1c
## Pacuta_HTHC_TP3_1418 #e31a1c
## Pacuta_HTHC_TP3_2527 #e31a1c
## Pacuta_HTHC_TP4_1169 #e31a1c
## Pacuta_HTHC_TP5_1168 #e31a1c
## Pacuta_ATAC_TP5_1059 #b15928
## Pacuta_HTHC_TP1_2210 #b15928
## Pacuta_HTAC_TP1_1653 #000000
## Pacuta_HTHC_TP6_1721 #000000
## Pacuta_ATAC_TP7_1445 #808080
## Pacuta_ATHC_TP10_1205 #808080
## Pacuta_ATHC_TP10_2550 #808080
## Pacuta_ATHC_TP6_1254 #808080
## Pacuta_HTHC_TP11_2185 #808080
## Pacuta_HTHC_TP5_1415 #808080
Load pairwise percent shared SNP results and convert if from one line per pair format into a symetric matrix uisng the xtabs function.
pairwise_percent_shared <- read.table("GVCFall.filtered.recode.vcf.gz.allelic_similarity.full.tsv", sep='\t', header=T)
pairwise_percent_shared.matrix <- xtabs(match_perc ~ ind1 + ind2, data=pairwise_percent_shared)
Process the simScore data ready for plotting (i.e., cluster samples based on computed distance and construct a dendrogram of the relationship).
# Make a copy of input matrix
tmp.mat <- pairwise_percent_shared.matrix
# Generate clusters from the allelic similarity scores matrix
tmp.mat.dist <- dist(tmp.mat, method="euclidean")
tmp.mat.hclust <- hclust(tmp.mat.dist, method="complete")
# Get sample colors for sidebar in the same order as the matrix
Rcols <- samples.info[rownames(tmp.mat),]$group_color
Ccols <- samples.info[colnames(tmp.mat),]$group_color
# Get min and max values of matrix
tmp.mat.min <- min(tmp.mat); tmp.mat.min
## [1] 76.25
tmp.mat.max <- max(tmp.mat); tmp.mat.max
## [1] 100
Plot clustering results and write dendrogram to file.
simScore.dendro <- as.dendrogram(tmp.mat.hclust)
write.dendrogram(simScore.dendro, "cluster_dendrogram.tre", edges=TRUE)
plot(tmp.mat.hclust)
Write ordered matrix to file incase we want it later.
tmp.mat.order <- dendro_data(simScore.dendro, type="rectangle")[["labels"]][["label"]]
tmp.mat.ordered <- tmp.mat[
order(match(rownames(tmp.mat), rev(tmp.mat.order))),
order(match(colnames(tmp.mat), tmp.mat.order))
]
write.table(as.matrix(tmp.mat.ordered),
"GVCFall.filtered.recode.vcf.gz.allelic_similarity.full.matrix.tsv",
sep='\t', quote=FALSE,
row.names=TRUE, col.names=TRUE)
Plot simScores heatmap.
par(cex.main=0.7, cex.lab=0.9, cex.axis=0.9) # Change the font size of the legend title, labels and axis
heatmap.2(x=tmp.mat,
Rowv = simScore.dendro,
Colv = simScore.dendro,
col=cividis(length(seq(75, 100, 0.1))-1),
breaks=seq(75, 100, 0.1),
trace="none", # Dont draw "trace" line
key=TRUE, # Show color-key
margins=c(8,8), # Numeric vector of length 2 containing the margins for column and row names, respectively.
ColSideColors=Ccols,
RowSideColors=Rcols,
offsetRow=0,
offsetCol=0,
cexRow=cexSize, # Positive numbers, used as cex.axis in for the row or column axis labeling.
cexCol=cexSize,
cellnote=formatC(tmp.mat, big.mark=","),
notecex=0.1,
)